Question

A decapeptide has the following amino acid composition. $$ \mathrm{Ala}_{2} \text {, Arg, Cys, Glu, Gly, Leu, Lys, Phe, Val } $$ Partial hydrolysis yields the following tripeptides. $$ \text { Cys-Glu-Leu + Gly-Arg-Cys + Leu-Ala-Ala + Lys-Val-Phe + Val-Phe-Gly } $$ One round of Edman degradation yields a lysine phenylthiohydantoin. From this information, deduce the primary structure of this decapeptide.

Short answer

Answer: The primary structure of the decapeptide is Lys-Val-Phe-Gly-Arg-Cys-Glu-Leu-Ala-Ala.

Step-by-step solution

Analyze the partial hydrolysis results

Partial hydrolysis breaks a peptide into smaller fragments (tripeptides in this case). We are given the following fragments: Cys-Glu-Leu Gly-Arg-Cys Leu-Ala-Ala Lys-Val-Phe Val-Phe-Gly Next, we will perform a step-by-step analysis to deduce the primary structure.

Identify the amino acid at the N-terminal

In the given information, one round of Edman degradation yields a lysine (Lys) phenylthiohydantoin. This indicates that lysine is at the N-terminal of the decapeptide.

Identify the fragment containing lysine

Since lysine is the N-terminal, look for a fragment starting with lysine. In this case, it is Lys-Val-Phe.

Connect the fragments

Now, we need to connect the remaining fragments sequentially. Looking at the fragments, we can deduce the connections as follows: 1. Val-Phe-Gly is the only fragment ending with Gly, so this fragment connects with the one starting with Gly, which is Gly-Arg-Cys. 2. After connection,we get Lys-Val-Phe-Gly-Arg-Cys. 3. The only fragment starting with Cys is Cys-Glu-Leu, so connect it: Lys-Val-Phe-Gly-Arg-Cys-Glu-Leu. 4. The only remaining fragment is Leu-Ala-Ala, and it starts with Leu, which is also the last amino acid in our current sequence. Connect it: Lys-Val-Phe-Gly-Arg-Cys-Glu-Leu-Ala-Ala.

Final primary structure

The primary structure of the decapeptide is: Lys-Val-Phe-Gly-Arg-Cys-Glu-Leu-Ala-Ala

Key concepts

Amino Acid Sequence

Understanding the amino acid sequence of a polypeptide or protein is like deciphering the unique code that dictates its function and structure. Each amino acid is akin to a letter in a long word, where the sequence defines the final shape and biological activity of the protein.

Amino acids are the building blocks of proteins, linked by peptide bonds to form polypeptides. The sequence of these molecules is what we call the primary structure, and it's critical because even a single change can have a significant impact on a protein's function, as seen in diseases like sickle-cell anemia.

When scientists are trying to deduce the amino acid sequence of a peptide, as in the case of the decapeptide in the exercise, they rely on methods like Edman degradation and partial hydrolysis to break down the peptide into smaller sequences or identify the terminal amino acids. With this data, they can then piece together the entire sequence, as if solving a jigsaw puzzle.

Edman Degradation

Edman degradation is a method employed by biochemists to determine the amino acid sequence at the start of a polypeptide chain. This stepwise process selectively removes the N-terminal amino acid of the peptide, which can then be identified.

The magic of Edman degradation lies in the fact that it doesn't destroy the rest of the polypeptide chain, allowing for repeated rounds to sequentially identify further residues at the N-terminus. During this process, the amino acid detached is converted into a stable derivative called a phenylthiohydantoin (PTH) amino acid, which can be easily identified using chromatography or electrophoresis.

In our textbook problem, Edman degradation revealed that lysine was the N-terminal amino acid, crucial information for beginning to solve the structure of the decapeptide.

Partial Hydrolysis

Partial hydrolysis is an analytical technique where water is used to cleave the peptide bonds between amino acids in a protein or peptide, but unlike complete hydrolysis, it stops at an intermediary stage. This results in a mixture of shorter oligopeptides rather than a pool of individual amino acids.

This technique is particularly valuable because it allows scientists to determine overlapping sequences and deduce the order of amino acids in a larger polypeptide. By comparing the resulting fragments, one can make educated guesses about the possible sequences and thus reconstruct the original chain.

In the exercise, partial hydrolysis generated several tripeptides, providing pieces of the puzzle that, when matched with the information from Edman degradation, allowed the students to successfully establish the full amino acid sequence of the decapeptide.